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Open data
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Basic information
Entry | Database: PDB / ID: 1yh2 | ||||||
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Title | Ubiquitin-Conjugating Enzyme HSPC150 | ||||||
![]() | HSPC150 protein similar to ubiquitin-conjugating enzyme | ||||||
![]() | LIGASE / STRUCTURAL GENOMICS CONSORTIUM / HSCP150 / UBIQUITIN / UBIQUITIN-CONJUGATING ENZYME / SGC | ||||||
Function / homology | ![]() protein K29-linked ubiquitination / protein K27-linked ubiquitination / protein K6-linked ubiquitination / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination ...protein K29-linked ubiquitination / protein K27-linked ubiquitination / protein K6-linked ubiquitination / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Fanconi Anemia Pathway / protein polyubiquitination / ubiquitin-protein transferase activity / DNA repair / ubiquitin protein ligase binding / DNA damage response / chromatin binding / nucleolus / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Walker, J.R. / Avvakumov, G.V. / Newman, E.M. / Mackenzie, F. / Kozieradzki, I. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-paganon, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen. Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.1 KB | Display | ![]() |
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PDB format | ![]() | 33.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.5 KB | Display | ![]() |
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Full document | ![]() | 427.6 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1y6lC ![]() 1yrvC ![]() 1zdnC ![]() 1zuoC ![]() 2a4dC ![]() 2a7lC ![]() 2awfC ![]() 2f4wC ![]() 2ob4C ![]() 2qgxC ![]() 2z5dC ![]() 3bzhC ![]() 3cegC ![]() 1jbbS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19345.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 4M Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 22, 2004 |
Radiation | Monochromator: confocal maxflux optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 19774 / Num. obs: 19774 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 44.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.266 / Num. unique all: 1885 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1JBB Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.483 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.992 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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